public void Add_one_chrom()
{
var position1 = new Mock <IPosition>();
position1.SetupGet(x => x.Chromosome).Returns(ChromosomeUtilities.Chr1);
position1.SetupGet(x => x.Start).Returns(100);
position1.SetupGet(x => x.RefAllele).Returns("A");
position1.SetupGet(x => x.AltAlleles).Returns(new [] { "C" });
var memStream = new MemoryStream();
using (var indexCreator = new OnTheFlyIndexCreator(memStream))
{
indexCreator.BeginSection("positions", 100);
indexCreator.Add(position1.Object, 2588);
indexCreator.EndSection("positions", 2699);
}
var readStream = new MemoryStream(memStream.ToArray());
readStream.Seek(0, SeekOrigin.Begin);
var index = new JasixIndex(readStream);
Assert.Equal(100, index.GetSectionBegin("positions"));
Assert.Equal(2588, index.GetFirstVariantPosition("chr1", 100, 102));
}
private void WriteOutput(IAnnotatedPosition annotatedPosition, long textWriterPosition,
OnTheFlyIndexCreator jasixIndexCreator, IJsonWriter jsonWriter, LiteVcfWriter vcfWriter,
LiteVcfWriter gvcfWriter, string jsonOutput)
{
jasixIndexCreator.Add(annotatedPosition.Position, textWriterPosition);
jsonWriter.WriteJsonEntry(jsonOutput);
if (vcfWriter == null && gvcfWriter == null || annotatedPosition.Position.IsRecomposed)
{
return;
}
string vcfLine = _conversion.Convert(annotatedPosition);
vcfWriter?.Write(vcfLine);
gvcfWriter?.Write(vcfLine);
}
public JsonWriter(StreamWriter writer, Stream indexStream, string annotator, string creationTime, string vepDataVersion,
List <IDataSourceVersion> dataSourceVersions, string genomeAssembly, string[] sampleNames, bool leaveOpen)
{
_writer = writer;
_writer.NewLine = "\n";
_firstEntry = true;
_positionFieldClosed = false;
_leaveOpen = leaveOpen;
_bgzipTextWriter = writer as BgzipTextWriter;
_jasixIndexCreator = _bgzipTextWriter != null
? new OnTheFlyIndexCreator(indexStream)
: null;
WriteHeader(annotator, creationTime, genomeAssembly, JsonCommon.SchemaVersion, vepDataVersion,
dataSourceVersions, sampleNames);
}
private ExitCodes ProgramExecution()
{
var sequenceProvider = ProviderUtilities.GetSequenceProvider(_refSequencePath);
var transcriptAnnotationProvider = ProviderUtilities.GetTranscriptAnnotationProvider(_inputCachePrefix, sequenceProvider);
var saProvider = ProviderUtilities.GetSaProvider(SupplementaryAnnotationDirectories);
var conservationProvider = ProviderUtilities.GetConservationProvider(SupplementaryAnnotationDirectories);
var refMinorProvider = ProviderUtilities.GetRefMinorProvider(SupplementaryAnnotationDirectories);
var geneAnnotationProvider = ProviderUtilities.GetGeneAnnotationProvider(SupplementaryAnnotationDirectories);
var plugins = PluginUtilities.LoadPlugins(_pluginDirectory);
var annotator = ProviderUtilities.GetAnnotator(transcriptAnnotationProvider, sequenceProvider, saProvider, conservationProvider, geneAnnotationProvider, plugins);
var recomposer = _disableRecomposition ? new NullRecomposer() : Recomposer.Create(sequenceProvider, _inputCachePrefix);
var logger = _outputFileName == "-" ? (ILogger) new NullLogger() : new ConsoleLogger();
var metrics = new PerformanceMetrics(logger);
var dataSourceVersions = GetDataSourceVersions(plugins, transcriptAnnotationProvider, saProvider,
geneAnnotationProvider, conservationProvider);
var vepDataVersion = transcriptAnnotationProvider.VepVersion + "." + CacheConstants.DataVersion + "." + SaDataBaseCommon.DataVersion;
var jasixFileName = _outputFileName + ".json.gz" + JasixCommons.FileExt;
using (var outputWriter = ReadWriteUtilities.GetOutputWriter(_outputFileName))
using (var vcfReader = ReadWriteUtilities.GetVcfReader(_vcfPath, sequenceProvider.RefNameToChromosome, refMinorProvider, _reportAllSvOverlappingTranscripts, recomposer))
using (var jsonWriter = new JsonWriter(outputWriter, _annotatorVersionTag, Date.CurrentTimeStamp, vepDataVersion, dataSourceVersions, sequenceProvider.GenomeAssembly.ToString(), vcfReader.GetSampleNames()))
using (var vcfWriter = _vcf ? new LiteVcfWriter(ReadWriteUtilities.GetVcfOutputWriter(_outputFileName), vcfReader.GetHeaderLines(), _annotatorVersionTag, vepDataVersion, dataSourceVersions) : null)
using (var gvcfWriter = _gvcf ? new LiteVcfWriter(ReadWriteUtilities.GetGvcfOutputWriter(_outputFileName), vcfReader.GetHeaderLines(), _annotatorVersionTag, vepDataVersion, dataSourceVersions) : null)
using (var jasixIndexCreator = new OnTheFlyIndexCreator(FileUtilities.GetCreateStream(jasixFileName)))
{
if (!(outputWriter is BgzipTextWriter bgzipTextWriter))
{
throw new NullReferenceException("Unable to create the bgzip text writer.");
}
try
{
jasixIndexCreator.SetHeader(jsonWriter.Header);
if (vcfReader.IsRcrsMitochondrion && annotator.GenomeAssembly == GenomeAssembly.GRCh37 ||
annotator.GenomeAssembly == GenomeAssembly.GRCh38 ||
_forceMitochondrialAnnotation)
{
annotator.EnableMitochondrialAnnotation();
}
int previousChromIndex = -1;
IPosition position;
var sortedVcfChecker = new SortedVcfChecker();
while ((position = vcfReader.GetNextPosition()) != null)
{
sortedVcfChecker.CheckVcfOrder(position.Chromosome.UcscName);
previousChromIndex = UpdatePerformanceMetrics(previousChromIndex, position.Chromosome, metrics);
var annotatedPosition = annotator.Annotate(position);
string json = annotatedPosition.GetJsonString();
if (json != null)
{
WriteOutput(annotatedPosition, bgzipTextWriter.Position, jasixIndexCreator, jsonWriter, vcfWriter, gvcfWriter, json);
}
else
{
gvcfWriter?.Write(string.Join("\t", position.VcfFields));
}
metrics.Increment();
}
WriteGeneAnnotations(annotator.GetAnnotatedGenes(), jsonWriter);
}
catch (Exception e)
{
e.Data[ExitCodeUtilities.VcfLine] = vcfReader.VcfLine;
throw;
}
}
metrics.ShowAnnotationTime();
return(ExitCodes.Success);
}
